Different OG Readings

I have an interesting problem. I boil 10 gal. batches in keggle with a recirculating pump. When I take gravity readings from the bottom of the kettle via the recirc line they are consistently 5-7 points lower than the readings when just skimming some wort of the top. These measurements are taken with both a calibrated hydrometer and refractometer. Both instruments reading match when taken from the same source. I always thought that 11 gallons of boiling wort would be pretty homogenous. Is there any chance that some stratification could be taking place or another reason I am getting varying, yet predicatable gravity readings?